def protein_step(self):
"""
Check mutations are valid
"""
self.start_timer()
if self.has(): # this is already done (very unlikely/
protein = system_storage[self.handle]
else:
log.info(
f'Step 1 analysis requested by {User.get_username(self.request)}'
)
uniprot = self.request.params['uniprot']
taxid = self.request.params['species']
mutation_text = self.request.params['mutation']
## Do analysis
mutation = Mutation(mutation_text)
protein = ProteinAnalyser(uniprot=uniprot, taxid=taxid)
protein.load()
protein.mutation = mutation
# assess
if not protein.check_mutation():
log.info('protein mutation discrepancy error')
discrepancy = protein.mutation_discrepancy()
self.reply = {
**self.reply, 'error': 'mutation',
'msg': discrepancy,
'status': 'error'
}
raise VenusException(discrepancy)
else:
system_storage[self.handle] = protein
self.reply['protein'] = self.jsonable(protein)
self.stop_timer()
def protein_step():
uniprot = request.params['uniprot']
taxid = request.params['species']
mutation = Mutation(request.params['mutation'])
protein = ProteinAnalyser(uniprot=uniprot, taxid=taxid)
try:
protein.load()
except FutureWarning:
log.error(
f'There was no pickle for uniprot {uniprot} taxid {taxid}. TREMBL code via API?'
)
#protein.__dict__ = ProteinGatherer(uniprot=uniprot, taxid=taxid).get_uniprot().__dict__
protein.mutation = mutation
if not protein.check_mutation():
log.info('protein mutation discrepancy error')
return {
'error': 'mutation',
'msg': protein.mutation_discrepancy(),
'status': 'error'
}
else:
handle = request.params['uniprot'] + request.params['mutation']
system_storage[handle] = protein
return {'protein': jsonable(protein), 'status': 'success'}